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Chembilikandy V, D'Mello A, Tettelin H, Martínez E, Orihuela CJ. Streamlining marker-less allelic replacement in Streptococcus pneumoniae through a single transformation step strategy: easyJanus. Appl Environ Microbiol 2024:e0101024. [PMID: 39140740 DOI: 10.1128/aem.01010-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/23/2024] [Indexed: 08/15/2024] Open
Abstract
The ability to genetically manipulate bacteria is a staple of modern molecular microbiology. Since the 2000s, marker-less mutants of Streptococcus pneumoniae (Spn) have been made by allelic exchange predominantly using the kanR-rpsL cassette known as "Janus." The conventional Janus protocol involves two transformation steps using multiple PCR-assembled products containing the Janus cassette and the target gene's flanking DNA. We present an innovative strategy to achieve marker-less allelic replacement through a single transformation step. Our strategy involves integrating an additional copy of the target's downstream region before the Janus cassette, leading to a modified genetic arrangement. This single modification reduced the number of required PCR fragments from five to four, lowered the number of assembly reactions from two to one, and simplified the transformation process to a single step. To validate the efficacy of our approach, we implemented this strategy to delete in Spn serotype 4 strain TIGR4 the virulence gene pspA, the entire capsular polysaccharide synthesis locus cps4, and to introduce a single-nucleotide replacement into the chromosome. Notably, beyond streamlining the procedure, our method markedly reduced false positives typically encountered during negative selection with streptomycin when employing the traditional Janus protocol. Furthermore, and as consequence of reducing the amount of exogenous DNA required for construct synthesis, we show that our new method is amendable to the use of commercially available synthetic DNA for construct creation, further reducing the work needed to obtain a mutant. Our streamlined strategy, termed easyJanus, substantially expedites the genetic manipulation of Spn facilitating future research endeavors. IMPORTANCE We introduce a new strategy aimed at streamlining the process for marker-less allelic replacement in Streptococcus pneumoniae, a Gram-positive bacterium and leading cause of pneumonia, meningitis, and ear infections. Our approach involves a modified genetic arrangement of the Janus cassette to facilitate self-excision during the segregation step. Since this new method reduces the amount of exogenous DNA required, it is highly amendable to the use of synthetic DNA for construction of the mutagenic construct. Our streamlined strategy, called easyJanus, offers significant time and cost savings while concurrently enhancing the efficiency of obtaining marker-less allelic replacement in S. pneumoniae.
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Affiliation(s)
- Vipin Chembilikandy
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Adonis D'Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eriel Martínez
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carlos J Orihuela
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
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Dao TH, Echlin H, McKnight A, Marr ES, Junker J, Jia Q, Hayden R, van Opijnen T, Isberg RR, Cooper VS, Rosch JW. Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones. mBio 2024; 15:e0282823. [PMID: 38193698 PMCID: PMC10865975 DOI: 10.1128/mbio.02828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Streptococcus pneumoniae is a major human pathogen of global health concern and the rapid emergence of antibiotic resistance poses a serious public health problem worldwide. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage and has remained rare. Our data indicate that deleterious fitness costs in the mammalian host constrain the emergence of fluoroquinolone resistance both by de novo mutation and recombination. S. pneumoniae was able to circumvent such deleterious fitness costs via the development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, resulting in a fitness benefit during infection of mice treated with fluoroquinolones. These data suggest that the emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes are an important contributor to the evasion of antibiotic-mediated killing.IMPORTANCEThe increasing prevalence of antibiotic resistant bacteria is a major global health concern. While many species have the potential to develop antibiotic resistance, understanding the barriers to resistance emergence in the clinic remains poorly understood. A prime example of this is fluroquinolone resistance in Streptococcus pneumoniae, whereby, despite continued utilization, resistance to this class of antibiotic remains rare. In this study, we found that the predominant pathways for developing resistance to this antibiotic class severely compromised the infectious capacity of the pneumococcus, providing a key impediment for the emergence of resistance. Using in vivo models of experimental evolution, we found that S. pneumoniae responds to repeated fluoroquinolone exposure by modulating key metabolic pathways involved in the generation of redox molecules, which leads to antibiotic treatment failure in the absence of appreciable shifts in resistance levels. These data underscore the complex pathways available to pathogens to evade antibiotic mediating killing via antibiotic tolerance.
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Affiliation(s)
- Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Abigail McKnight
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Enolia S. Marr
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Julia Junker
- Nationales Referenzzentrum für Streptokokken Abteilung Medizinische Mikrobiologie, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ralph R. Isberg
- Deptartment of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Vaughn S. Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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Ganaie FA, Saad JS, Lo SW, McGee L, van Tonder AJ, Hawkins PA, Calix JJ, Bentley SD, Nahm MH. Novel pneumococcal capsule type 33E results from the inactivation of glycosyltransferase WciE in vaccine type 33F. J Biol Chem 2023; 299:105085. [PMID: 37495106 PMCID: PMC10462825 DOI: 10.1016/j.jbc.2023.105085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
The polysaccharide (PS) capsule is essential for immune evasion and virulence of Streptococcus pneumoniae. Existing pneumococcal vaccines are designed to elicit anticapsule antibodies; however, the effectiveness of these vaccines is being challenged by the emergence of new capsule types or variants. Herein, we characterize a newly discovered capsule type, 33E, that appears to have repeatedly emerged from vaccine type 33F via an inactivation mutation in the capsule glycosyltransferase gene, wciE. Structural analysis demonstrated that 33E and 33F share an identical repeat unit backbone [→5)-β-D-Galf2Ac-(1→3)-β-D-Galp-(1→3)-α-D-Galp-(1→3)-β-D-Galf-(1→3)-β-D-Glcp-(1→], except that a galactose (α-D-Galp) branch is present in 33F but not in 33E. Though the two capsule types were indistinguishable using conventional typing methods, the monoclonal antibody Hyp33FM1 selectively bound 33F but not 33E pneumococci. Further, we confirmed that wciE encodes a glycosyltransferase that catalyzes the addition of the branching α-D-Galp and that its inactivation in 33F strains results in the expression of the 33E capsule type. Though 33F and 33E share a structural and antigenic similarity, our pilot study suggested that immunization with a 23-valent pneumococcal PS vaccine containing 33F PS did not significantly elicit cross-opsonic antibodies to 33E. New conjugate vaccines that target capsule type 33F may not necessarily protect against 33E. Therefore, studies of new conjugate vaccines require knowledge of the newly identified capsule type 33E and reliable pneumococcal typing methods capable of distinguishing it from 33F.
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Affiliation(s)
- Feroze A Ganaie
- Division of Pulmonary/Allergy/Critical Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andries J van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paulina A Hawkins
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA; CDC Foundation, Atlanta, Georgia, USA
| | - Juan J Calix
- Division of Pulmonary/Allergy/Critical Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA; Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Moon H Nahm
- Division of Pulmonary/Allergy/Critical Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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Echlin H, Iverson A, Sardo U, Rosch JW. Airway proteolytic control of pneumococcal competence. PLoS Pathog 2023; 19:e1011421. [PMID: 37256908 PMCID: PMC10259803 DOI: 10.1371/journal.ppat.1011421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 06/12/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic pathogen that colonizes the upper respiratory tract asymptomatically and, upon invasion, can lead to severe diseases including otitis media, sinusitis, meningitis, bacteremia, and pneumonia. One of the first lines of defense against pneumococcal invasive disease is inflammation, including the recruitment of neutrophils to the site of infection. The invasive pneumococcus can be cleared through the action of serine proteases generated by neutrophils. It is less clear how serine proteases impact non-invasive pneumococcal colonization, which is the key first step to invasion and transmission. One significant aspect of pneumococcal biology and adaptation in the respiratory tract is its natural competence, which is triggered by a small peptide CSP. In this study, we investigate if serine proteases are capable of degrading CSP and the impact this has on pneumococcal competence. We found that CSP has several potential sites for trypsin-like serine protease degradation and that there were preferential cleavage sites recognized by the proteases. Digestion of CSP with two different trypsin-like serine proteases dramatically reduced competence in a dose-dependent manner. Incubation of CSP with mouse lung homogenate also reduced recombination frequency of the pneumococcus. These ex vivo experiments suggested that serine proteases in the lower respiratory tract reduce pneumococcal competence. This was subsequently confirmed measuring in vivo recombination frequencies after induction of protease production via poly (I:C) stimulation and via co-infection with influenza A virus, which dramatically lowered recombination events. These data shed light on a new mechanism by which the host can modulate pneumococcal behavior and genetic exchange via direct degradation of the competence signaling peptide.
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Affiliation(s)
- Haley Echlin
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Amy Iverson
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Ugo Sardo
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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York A, Huynh E, Mbodj S, Yolda-Carr D, Hislop MS, Echlin H, Rosch JW, Weinberger DM, Wyllie AL. Magnetic bead-based separation of pneumococcal serotypes. CELL REPORTS METHODS 2023; 3:100410. [PMID: 36936076 PMCID: PMC10014298 DOI: 10.1016/j.crmeth.2023.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/18/2022] [Accepted: 01/26/2023] [Indexed: 02/23/2023]
Abstract
The separation of pneumococcal serotypes from a complex polymicrobial mixture may be required for different applications. For instance, a minority strain could be present at a low frequency in a clinical sample, making it difficult to identify and isolate by traditional culture-based methods. We therefore developed an assay to separate mixed pneumococcal samples using serotype-specific antiserum and a magnetic bead-based separation method. Using qPCR and colony counting methods, we first show that serotypes (12F, 23F, 3, 14, 19A, and 15A) present at ∼0.1% of a dual serotype mixture can be enriched to between 10% and 90% of the final sample. We demonstrate two applications for this method: extraction of known pneumococcal serotypes from saliva samples and efficient purification of capsule switch variants from experimental transformation experiments. This method may have further laboratory or clinical applications when the selection of specific serotypes is required.
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Affiliation(s)
- Anna York
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Emily Huynh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sidiya Mbodj
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Maikel S. Hislop
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Life Sciences and Chemistry, Utrecht University of Applied Sciences, 3584 CS Utrecht, the Netherlands
| | - Haley Echlin
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jason W. Rosch
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel M. Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Rep 2022; 41:111835. [PMID: 36516783 PMCID: PMC9850807 DOI: 10.1016/j.celrep.2022.111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.
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Affiliation(s)
- Andrew T. Nishimoto
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, MA 02467, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Lead contact,Correspondence:
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